Hello!
Deepdwn does use a (local) sqlite database exclusively for tracking word count changes over time (for this feature). It contains only a word count, timestamp and filename.
For everything else, the markdown files themselves are the source of truth, and are processed when launching Deepdwn. This includes the content of your files for search and display, all file tagging and categorization, directory structure, and all other metadata (whether a document is pinned, or enforces a right-to-left direction, etc). This is actually one of Deepdwn’s core features/principles.
That said, there are some features that I would like to add that will rely on either external files or a database, namely more powerful search tools, and edit history storage that can’t realistically be stored in markdown(+yaml), so those may be added in the future.